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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqFeatCollection.t 16151 2009-09-22 16:52:29Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 24,
-requires_module => 'DB_File');
use_ok('Bio::SeqFeature::Collection');
use_ok('Bio::Location::Simple');
use_ok('Bio::Tools::GFF');
use_ok('Bio::SeqIO');
}
my $verbose = test_debug();
#First of all we need to create an flat db
my $simple = Bio::SeqIO->new(-format => 'genbank',
-file => test_input_file('AB077698.gb'));
my @features;
my $seq = $simple->next_seq();
@features = $seq->top_SeqFeatures();
is(scalar @features, 11);
my $col = Bio::SeqFeature::Collection->new(-verbose => $verbose);
ok($col);
is($col->add_features( \@features), 11);
my @feat = $col->features_in_range(-range => ( Bio::Location::Simple->new
(-start => 100,
-end => 300,
-strand => 1) ),
-contain => 0);
is(scalar @feat, 5);
if( $verbose ) {
foreach my $f ( @feat ) {
print "location: ", $f->location->to_FTstring(), "\n";
}
}
is(scalar $col->features_in_range(-range => ( Bio::Location::Simple->new
(-start => 100,
-end => 300,
-strand => -1) ),
-strandmatch => 'ignore',
-contain => 1), 2);
@feat = $col->features_in_range(-start => 79,
-end => 1145,
-strand => 1,
-strandmatch => 'strong',
-contain => 1);
is(scalar @feat, 5);
if( $verbose ) {
foreach my $f ( sort { $a->start <=> $b->start} @feat ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
}
is($feat[0]->primary_tag, 'CDS');
ok($feat[0]->has_tag('gene'));
$verbose = 0;
# specify input via -fh or -file
my $gffio = Bio::Tools::GFF->new(-file => test_input_file('myco_sites.gff'),
-gff_version => 2);
@features = ();
# loop over the input stream
while(my $feature = $gffio->next_feature()) {
# do something with feature
push @features, $feature;
}
$gffio->close();
is(scalar @features, 412);
$col = Bio::SeqFeature::Collection->new(-verbose => $verbose,
-usefile => 1);
ok($col);
is($col->add_features( \@features), 412);
my $r = Bio::Location::Simple->new(-start => 67700,
-end => 150000,
-strand => 1);
@feat = $col->features_in_range(-range => $r,
-strandmatch => 'ignore',
-contain => 0);
is(scalar @feat, 56);
is($col->feature_count, 412);
my $count = $col->feature_count;
$col->remove_features( [$features[58], $features[60]]);
is( $col->feature_count, 410);
@feat = $col->features_in_range(-range => $r,
-strandmatch => 'ignore',
-contain => 0);
is( scalar @feat, 54);
# add the removed features back in in order to get the collection back to size
$col->add_features([$features[58], $features[60]]);
# let's randomize so we aren't removing and adding in the same order
# and hopefully randomly deal with a bin's expiration
fy_shuffle(\@features);
foreach my $f ( @features ) {
$count--, next unless defined $f;
$col->remove_features([$f]);
# ok( $col->feature_count, --$count);
}
is($col->feature_count, 0);
# explicitly destroy old instances above (should clear out any open filehandles
# w/o -keep flag set)
undef $col;
my $filename = test_output_file();
my $newcollection = Bio::SeqFeature::Collection->new(-verbose => $verbose,
-keep => 1,
-file => $filename);
$newcollection->add_features(\@feat);
is($newcollection->feature_count, 54);
undef $newcollection;
ok(-s $filename);
$newcollection = Bio::SeqFeature::Collection->new(-verbose => $verbose,
-file => $filename);
is($newcollection->feature_count, 54);
undef $newcollection;
ok( ! -e $filename);
# without -keep => 1, $filename was deleted as expected.
# to stop Bio::Root::Test complaining that the temp file was already deleted,
# we'll just create it again
open(TMP, ">", $filename);
print TMP "temp\n";
close(TMP);
if( $verbose ) {
my @fts = sort { $a->start <=> $b->start}
grep { $r->overlaps($_,'ignore') } @features;
if( $verbose ) {
foreach my $f ( @fts ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
print "\n";
}
my %G = map { ($_,1) } @feat;
my $c = 0;
foreach my $A ( @fts ) {
if( ! $G{$A} ) {
print "missing ", $A->primary_tag, " ", $A->location->to_FTstring(), "\n";
} else {
$c++;
}
}
print "Number of features correctly retrieved $c\n";
foreach my $f ( sort { $a->start <=> $b->start} @feat ) {
print $f->primary_tag, " ", $f->location->to_FTstring(), "\n";
}
}
sub fy_shuffle {
my $array = shift;
my $i;
for( $i = @$array; $i--; ) {
my $j = int rand($i+1);
next if $i==$j;
@$array[$i,$j] = @$array[$j,$i];
}
}
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